FIG. 1 shows a typical arrangement 100 for conducting capillary electrophoresis. A capillary 102 having a window region 104 has its ends dipped in buffer 106. A sample 108 to be electrophoresced is introduced at one of the capillary's ends and a voltage differential is applied across the two ends. This causes the sample 108 to separate into its components, each of which migrate at different rates in the direction depicted by the arrow. A laser light source 110 is used to illuminate the samples, which typically are tagged with a chromophore. In response to this excitation, the samples emit light 112 which is then captured by a camera 114, after which the results are processed by a computer 116.
In the configuration described, the capillaries are used a number of times before they are discarded. Without some form of capillary cleaning, however, a small quantity of a sample, such as protein, may get absorbed on the inner wall of the capillary, thereby contaminating a subsequent electrophoresis run. Therefore, between each electrophoresis run, a capillary is typically rinsed, usually under high pressure. Although a variety of cleaning solutions may be employed to rinse a capillary, one of the more popular rinses is NaOH, such as in the concentration of 50 mM to 200 mM. The NaOH solution is pumped through the capillaries to help remove residual traces of the electrophoretic medium and the sample which migrated therein.